Wrong Tree Format

[GoogleCodeExporter]

What steps will reproduce the problem?
1. run prottest3 with a >4K sequence alignment 
2. java -jar $PROTTEST_HOME/prottest-3.4.jar -i HYDRO_Hits.fasta.block  
-all-distributions  -BIC -threads 1 -log enabled

What is the expected output? What do you see instead?

ProtTest 3.2                        Fast selection of the best-fit models of 
protein evolution
(c) 2009-2010   Diego Darriba (1,2), Guillermo Taboada (2), Ramón Doallo (2), 
David Posada (1)
(1)                               Facultad de Biologia, Universidad de Vigo, 
36200 Vigo, Spain
(2)                    Facultade de Informática, Universidade da Coruña, 
15071 A Coruña, Spain
Contact:                                                     ddarriba@udc.es, 
dposada@uvigo.es
--------------------------------------------------------------------------------
--------------

Fri Oct 24 10:48:16 EDT 2014
OS = Linux (2.6.32-358.11.1.el6.x86_64)

Citation: Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection 
of best-fit 
          models of protein evolution. Bioinformatics, 27:1164-1165, 2011

ProtTest options
----------------
  Alignment file........... : HYDRO_Hits.fasta.block
  Tree..................... : BioNJ
  StrategyMode............. : Fixed BIONJ JTT
  Candidate models......... : 
    Matrices............... : JTT LG DCMut MtREV MtMam MtArt Dayhoff WAG RtREV CpREV Blosum62 VT HIVb HIVw FLU 
    Distributions.......... : +G +I +I+G Uniform 
    Observed frequencies... : false

  Statistical framework
    Sort models according to....: 
       BIC 
    Sample size.................: 338.0 (not calculated yet)
  Other options:
    Display best tree in ASCII..: false
    Display best tree in Newick.: false
    Display consensus tree......: false
    Verbose.....................: false

Phyml's exit value: 1 (there was probably some error)
Phyml's command-line: 
/n/sw/centos6/prottest-3.4-20140123/bin/phyml-prottest-linux64    -i 
/tmp/prottest_alignment_2686744625070301904.tmp -c 1 -m JTT -v 0.0   -o r -f d  
 -d aa -b 0   --no_memory_check     
Please, take a look at the Phyml's log below:
ProtTest: wrong tree format, exiting...

What version of the product are you using? On what operating system?

Running on Centos 6

Please provide any additional information below.

I have two alignement, that were generated in the exact same way, one has 1.2K 
sequences the other one has 4k sequence. 
The 1.2K sequence file works fine, but the 4K file crashes. 
I have tried Phylip, nexus, Fasta formats no change. 
I do not understand what is the problem. 

I have attached the alignement.

Original issue reported on code.google.com by ledjfou125 on 24 Oct 2014 at 3:03

Attachments:

• HYDRO_Hits.fasta.block

[GoogleCodeExporter]

Original comment by DiegoDL84 on 29 Oct 2014 at 9:35

• Changed state: Accepted

[GoogleCodeExporter]

PhyML cannot handle such a big alignment. If I'm not wrong, there are 2 
constraints for the alignment size in PhyML: There is a limit of 4,000 taxa, 
and NTAXA * NTAXA * SEQLEN should not be greater than 10^8. I'm sorry about 
that.

Original comment by DiegoDL84 on 29 Oct 2014 at 9:43

• Changed state: WontFix